The many new and varied assays for molecular detection of respiratory viruses make today “an excellent time to be working in infectious diseases,” says Dr. Christine Ginocchio.

William Check, PhD

When it comes to molecular detection of respiratory viruses, laboratorians today have an embarrassment of riches. “This talk would have been very different five years ago,” Christine C. Ginocchio, PhD, MT(ASCP), said at last year’s Association for Molecular Pathology meeting at the outset of her review of multianalyte platforms for detecting respiratory viruses. The advances in this area have been substantial, she told CAP TODAY recently, adding: “There has been an explosion of molecular assays, both IVD cleared and not.” Dr. Ginocchio, who is senior medical director and chief, Division of Infectious Disease Diagnostics, Department of Pathology and Laboratory Medicine, North Shore-LIJ Health System Laboratories in New York, calls this “an excellent time to be working in infectious diseases.”

“We now have several FDA-cleared assays for detection of multiple respiratory viruses in the same sample, and they have a wide range of multiplexity,” she says.

With so many platforms available—Dr. Ginocchio discussed 13, seven cleared and six in trials—and with such a wide range in multiplexity, turnaround time, throughput, degree of automation, and cost, how is a lab to know which system best fits its needs? Or, for that matter, whether it even needs a multiplex platform? Laboratorians might follow the real estate mantra: “Location, location, location.”

“It would seem that use of the new viral panels would be a no-brainer, but that is not the case,” says Richard B. Thomson, PhD, medical director of the microbiology laboratories at Evanston (Ill.) Hospital of NorthShore University Health-System and clinical professor of pathology, University of Chicago. Reagent expense is a major reason, Dr. Thomson told CAP TODAY, as is capital expense. That makes it crucial to think about where specimens are coming from. “Right now there are many different outpatient and inpatient settings where viral diagnostics are used,” Dr. Thomson says, and acuity of disease and viral pathogens vary among them.

“Let’s say,” he continues, “an adult comes into a doctor’s office in the middle of February with lots of influenza virus circulating in the community. Do you need an influenza-only test or do you do an assay that detects 14 viruses? No test is cheap.” For decades clinical microbiologists have tried to do things cost-effectively. “Now we are trying to figure out the best way to use these new tests. Some say they are wonderful, use them all the time. Others prefer to use them only for acutely ill patients who are admitted. I’m still hesitant to plug them into everybody.”

Dr. Thomson’s colleague at Evanston Hospital, Karen Kaul, MD, PhD, is also thinking about how best to take advantage of multiplex molecular platforms for respiratory viruses. “There is increasing interest in more broadly characterizing the full array of respiratory viruses in patients with influenza-like illness,” says Dr. Kaul, board of directors chair of molecular pathology and director of the molecular diagnostics laboratory, as well as clinical professor of pathology, University of Chicago. “The jury is still out on how quickly we need that information. For some viruses—influenza, parainfluenza, adenovirus, respiratory syncytial virus—it would be nice to get data quickly because patients need to be isolated if they are admitted. So there is pressure on the lab to provide both breadth and speed.”

Their experience with many broad respiratory virus platforms has made it clear they can require more work, she says. “And they are less sensitive than individual real-time PCRs. So we need to think carefully about whether we are giving up clinically important sensitivity when moving from straight flu PCR to a multiplex platform.”

Dr. Kaul cites the old adage about balancing speed, cost, and accuracy. “That is kind of where we’re at,” she says, summing up their evaluation of multiplex platforms. “Real-time PCR is relatively accurate and cheap, but you have to run it in batches. [Idaho Technology’s] FilmArray is expensive and perhaps less sensitive [than real-time PCR], but it is fast. And GenMark [eSensor], and I suspect Luminex [xTAG RVP], will be somewhere in the middle.” So, “Different answers for different institutions and settings,” she says.

Indeed, different solutions for different settings emerged as a universal theme from interviews with laboratorians.

Two other themes emerged from these interviews. First, rapid antigen tests are suboptimal. In an interview, Karen M. Frank, MD, PhD, the second speaker in the AMP session, acknowledged the 15- to 60-minute turnaround time of rapid antigen tests. “The problem,” she said, “as we have recognized more recently, is that those assays are limited in sensitivity and specificity.” The low accuracy of rapid antigen tests had been underestimated previously because they were compared with culture, rather than with the more accurate molecular tests, says Dr. Frank, who is director of the University of Chicago Medical Center clinical microbiology and immunology laboratories and associate professor, Department of Pathology, University of Chicago.

Second, every laboratory should strive to incorporate molecular tests into their respiratory virus testing menu, at least for selected patient populations. “Molecular testing has definitely changed clinical practice in certain patient groups,” Dr. Frank says, citing immunocompromised inpatients as an example. “Molecular tests offer more reliable results and physicians are changing therapy based on them. In the outpatient and emergency department population there is a lot of empiric therapy. So molecular testing is not thought by many to be as essential.”

“There is no question that molecular is the way to go,” says Robert C. Jerris, PhD, D(ABMM), medical director of microbiology at Children’s Healthcare of Atlanta. “Molecular tests that return results in one or two hours have had a dramatic impact on patient care.” Dr. Jerris favors them, for certain assays, for large pediatric facilities, such as his, even in the ED. “The quality and performance of the assays out there now are very robust,” he says. “We need to meet the needs of our patient populations. As available [molecular] test systems and reagents expand, we will be able to do that.”

Dr. Chapin, too, sees molecular methods as the prevailing standard. She recently did an extensive evaluation of commercial molecular platforms for respiratory virus testing, which she described in a talk on the Web site of the American Society for Microbiology (http://clinmicro.asm.org/images/archive/2012-02_chapinppt.pdf). “Many companies are coming out with rapid molecular tests that can replace rapid antigen tests in the emergency department,” Dr. Chapin, professor of pathology and medicine at Alpert Brown Medical School, told CAP TODAY. As an example, she points to the Liat Iquum assay for flu A/B, which she says costs $50 per test and provides a result in 20 minutes.

“Years ago only sophisticated virology labs could respond quickly to an outbreak with a single, virus-specific PCR,” Dr. Chapin says. “Luminex RVP is still the classic multiplex platform, but it is not particularly user-friendly and it takes six to eight hours to run.” Simple, rapid molecular assays now becoming available, such as the Iquum and Cepheid’s Xpert Flu, may provide a satisfactory solution to the need for a rapid influenza test for acute care, she says.

Still, these advances come at a price. “When I give talks I stress that nothing is cheap in our molecular micro lab compared to what we used to do,” Dr. Chapin says. Her advice: “Pair with infection control and infectious disease. Get them to support your application.”

Dr. Jerris, too, suggests getting colleagues on board before going to administration. “My biggest recommendation is plan, plan, plan,” he says. “Then communicate with your end users and put a package together that works for them.”

Alexandra Valsamakis, MD, PhD, followed that course and ended up feeling like “Woman of the Year” among her clinical clients at Johns Hopkins Medical Institutions. When Dr. Valsamakis, who is associate professor of pathology and director of clinical virology and molecular microbiology, got ready to institute a multiplex molecular platform, she says, “I literally took my dog-and-pony show for six weeks to many clinical services. It was such a dramatic change from what we had done for a long time. When we finally flipped the switch, we all sat here in the office waiting for the phones to light up. And it was as quiet as a church.”

Randall Hayden, MD, moderator of the AMP session, told CAP TODAY that one reason for selecting the multianalyte testing topic was that the time is ripe for use of panels for respiratory viruses. “Between six and 20 agents are known that may have clinical significance,” says Dr. Hayden, director of clinical and molecular microbiology in the Department of Pathology, St. Jude Children’s Research Hospital. “For most or all of these viruses, molecular methods have been shown to increase sensitivity. In that setting, it is more cost-effective and labor efficient to use a multiplex platform.”

At the same time, Dr. Hayden calls the many viruses on some large panels “to a certain extent, targets of opportunity.” They are there because they can be put there. “There are a limited number of clinical settings where such a broadly multiplexed system will have clinical impact,” he says. “Use of panels for targeting therapy may be less important than perhaps for being able to reduce unnecessary use of antimicrobials.” In a hospital for children with cancer, such as St. Jude, physicians may cover for bacterial agents, even with the detection of a virus. In such a setting, timely isolation for infection control could still be a benefit.

Dr. Hayden’s laboratory uses primarily real-time PCR tests, both in-house and commercial. In specific circumstances, direct fluorescence antibody (DFA) and culture may be brought into play. “We are reasonably certain we will end up using one of the multiplex systems in some circumstances on some patients,” Dr. Hayden says. In his view, the field has not yet reached a consensus on when, or whether, to trade the greater sensitivity of individual real-time PCRs for panels. “We are still learning how to use these platforms,” he says. “Certainly there is room for both modes of testing.”

In her AMP talk, Dr. Ginocchio, who is a professor at Hofstra University North Shore-LIJ School of Medicine, noted that current platforms have “many levels of multiplexity, throughput, and degree of work—from manual extraction to sample in, result out.” FilmArray has the highest multiplexity, with 15 viruses or subtypes. Luminex includes 12 viruses or subtypes in the original panel and eight in the Fast assay. (Coronaviruses and parainfluenza 4 are approved in Europe but not FDA cleared in the United States for clinical testing.)

FilmArray is the quintessential black box. “We have gone from the labor-intensive Luminex xTAG RVP to the simple FilmArray that can bring molecular testing to any sized hospital laboratory,” Dr. Ginocchio said. FilmArray also has a fast TAT, about one and a half hours, whereas a Luminex run takes about eight hours. But the Luminex RVP assay can test many samples at a time; FilmArray handles one at a time per unit. “Therefore, for high-volume laboratories the FilmArray system is limited due to low throughput,” she says.

Frank Zhang, MD, manager of R&D, molecular diagnostics; Ryhana Manji, BS, laboratory technologist, molecular diagnostics; and Dr. Ginocchio (rear) at the North Shore-LIJ Health System Laboratories, where Luminex is used for routine testing. Soon the laboratories on site in the health system’s 11 hospitals will have FilmArrays.

Dr. Ginocchio’s core laboratory relies on Luminex for routine testing. All patients admitted to the hospital receive a full Luminex panel. During respiratory season, she estimates her laboratory tests about 25,000 to 35,000 samples. Because of FilmArray’s low throughput, Dr. Ginocchio says, “If we ran FilmArray in the core lab, we would need so many instruments we wouldn’t have space for them.”

However, FilmArray will soon have a place in the on-site laboratories in the 11 hospitals in the North Shore-LIJ Health System. They have been using rapid antigen tests for flu A/B and RSV screening; all samples, positive or negative, are reflexed to the core lab for workup on Luminex. Next season, Dr. Ginocchio says, they will decentralize the respiratory virus testing by providing each on-site laboratory with a FilmArray to use at the point of care. Currently, “If they need results stat, they send the sample directly to the core lab and we do DFA for eight respiratory viruses with a turnaround time of a few hours,” she says, adding that the full RVP panel results are guaranteed in 24 hours. However, with the approval of FilmArray, the testing can now be performed within two hours at each hospital rapid-response laboratory. Since FilmArray has lower sensitivity for adenovirus, that analyte will be supplemented with PCR in high-risk populations (oncology, solid organ and bone marrow transplantation). Luminex is also “a bit suboptimal for adeno,” Dr. Ginocchio says, and it too is supplemented with culture, to be replaced this year with PCR. “We are awaiting FDA approval of a new adenovirus PCR from Argene [acquired by BioMérieux],” she told CAP TODAY. “Then we will add the PCR, which is more sensitive.”

Dr. Frank subtitled her AMP talk “The Reality Check” after reading a comment from one of the respondents to a survey she conducted among ClinMicroNet users on testing for respiratory viruses. “Here is a Reality Check for you, Karen!” this laboratorian wrote. “Resources are limited. We function without molecular tests.” Interestingly, only 20 of the 29 labs that responded were using molecular methods even though, as Dr. Frank noted, “the group is skewed toward academic labs.”

Dr. Frank shared CAP Surveys data from 2009–2011. A few hundred laboratories use DFA and culture, but about 2,000 continue to use rapid antigen assays. Only a few hundred use molecular methods for influenza or respiratory syncytial virus. “There is a national controversy over rapid antigen testing,” Dr. Frank said in a recent interview. “Some people who have thought very hard still think there’s a place for it. I disagree. I think it’s worse to use it.” In her presentation Dr. Frank showed three prototypical cases (for example: “Isolation and Cohorting” in a two-year-old admitted for respiratory symptoms) demonstrating that false-positive or false-negative results from rapid antigen tests are not harmless (see box).

Dr. Frank’s laboratory at the University of Chicago stopped using rapid antigen tests for flu in 2008 and RSV in 2010, and stopped using DFA in 2009. It will discontinue viral culture this year. “We used DFA for a long time,” Dr. Frank says. “It’s actually faster than some molecular assays. But it’s not as sensitive or specific.” Testing now relies on Luminex RVP and on Prodesse RSV and Flu A/B. Because of the shortcomings of many technologies for adenovirus, which is potentially lethal in immunocompromised patients, Dr. Frank keeps shell vial available for this pathogen and is validating an individual real-time PCR for adenovirus.

Most recently, Dr. Frank purchased a FilmArray for its rapidity of results and ease of use. Prodesse is done on Monday, Wednesday, and Friday, Luminex on Tuesday and Friday. Film-Array will provide testing capability on the weekend and in immunocompromised oncology patients during off hours.

Even with its high capital and reagent costs (about $100 per test), multiplex molecular assays can be cost-effective, according to a cost analysis that compared various combinations of Luminex RVP and DFA for respiratory viruses (Mahony JB, et al. J Clin Microbiol. 2009;47:2812–2817). Taking into account total hospital costs, the molecular method was least costly for viral prevalence above 11 percent, which will typically be the case.

At about the time of the 2009 swine flu pandemic, Dr. Chapin switch-ed from a combination of rapid antigen, DFA, and shell vial in the emergency department to Luminex RVP. “It quickly became obvious we couldn’t give emergency department physicians a fast enough result using a panel assay,” she says. “So we implemented a rapid PCR for influenza.” One low-volume hospital in the Lifespan system uses Cepheid Flu A/B, not reporting the H1N1 component. Dr. Chapin may adopt a faster 20-minute PCR, such as Liat Iquum. “In a side-by-side comparison they were equivalent,” she says. However, the Iquum can do only one test at a time whereas the Cepheid takes multiple cartridges.

In her core laboratory Dr. Chapin uses the Luminex platform on admitted patients. “Subsequent to the pandemic it became clear that over half of patients admitted for influenza-like illness actually had something other than influenza,” she told CAP TODAY. “That sold me on molecular panels for hospitalized patients.” As she said in her talk, “Flu season is not just flu.” Moreover, her infection control colleagues like having a specific diagnosis for purposes of cohorting patients.

FilmArray’s lower throughput “wouldn’t cut it for me,” Dr. Chapin says. Her in-season volume is too high—15 to 50 specimens per day. In an eight-hour shift FilmArray does eight specimens, while Luminex can do up to 80. “Would I implement FilmArray in addition to Luminex?” she asks. “It might make a perfect complement off-season in immunocompromised patients.”

Dr. Chapin sees a specific molecular diagnosis, in addition to facilitating cohorting, as being valuable in guiding therapy—in a negative way. “What I am trying to get clinicians to do is not prescribe antibiotics when they are not needed,” she says. “I want them to get the therapeutic intervention right at the start.” That’s a difficult goal, she notes, especially in children, where acute otitis media and sinusitis are preceded by a viral infection 35 percent to 40 percent of the time.

“My ideal molecular assay for my setting would be flu, RSV, and rhino,” Dr. Chapin says. “This combination would address pediatrics, the elderly, and acute care patients.” It would cover the most common virus (over 50 percent of patients admitted for respiratory illness have rhinovirus), treatable viruses, and RSV (the pathogen for which it’s most helpful to cohort patients).

Marie Louise Landry, MD, director of the Yale University clinical virology laboratory and professor and vice chair, Department of Laboratory Medicine, Yale University School of Medicine, is still looking for a satisfactory multiplex platform. “We do single in-house real-time PCRs—10 respiratory viruses in six reactions—twice a day during respiratory season, which is very labor-intensive,” she said in an interview. Until recently Dr. Landry’s firstline method was DFA, which performs well compared with culture and even some PCR assays. However, she explains, “Last year we did a comparison of DFA to our current PCR panel on inpatients. DFA did not perform as well as we thought. We have a lot of older people in ICUs who have a lower titer of virus. That’s where you see the value of PCR.” She now considers PCR the standard for hospitalized patients.

With stress on the lab to accommodate testing with multiple PCR assays, she and colleagues were interested in finding a commercial method with several viruses in one tube to replace their in-house PCR. They tried a flu A/B/RSV real-time PCR kit. The sensitivity for RSV was only about 90 percent compared with the lab’s PCR assay. For flu A it was 87 percent and for flu B 82 percent. “Many of the missed positives were from very sick patients,” Dr. Landry says. She had set a sensitivity of 95 percent as the cutoff to make a switch. “We were very disappointed that it didn’t meet that criterion.”

Dr. Landry also finds highly multiplexed kits that are FDA approved to be less sensitive than her current tests. Also, some have a throughput that is too low. And she was concerned that highly multiplexed assays that use conventional PCRs have a higher risk of contamination. “We just didn’t want to go backward,” she says.

Dr. Landry has another concern: “You lose the quantitation that you get with real-time PCR by using the cycle threshold, which helps identify the main pathogen.” She describes one immunocompromised patient who was positive for adenovirus, cytomegalovirus, and rhinovirus. “The adenovirus signal was very strong, at 16 cycles, while CMV was 36 cycles,” Dr. Landry says. “Rhinovirus started in the mid-20s and went up to 39 after a few days, while adenovirus remained at 16 cycles. That allowed us to identify the predominant pathogen. Once you have something [that works so well], it’s hard to give it up.”

Dr. Valsamakis adopted Luminex RVP in the wake of the swine flu pandemic. Her laboratory at Johns Hopkins was doing DFA, shell vial, and tube culture on all specimens. “It became very clear we couldn’t sustain that algorithm,” Dr. Valsamakis says. “We got hit by an extraordinary number of specimens. The lab just wilted. We couldn’t keep up the labor required.” She devised a new approach and spent the summer and fall of 2009 selling it to the clinicians. In November 2009, it went live.

“Everyone who gets a swab submitted for respiratory viruses gets DFA for eight viruses,” Dr. Valsamakis says. Turnaround time is two to three hours. “If we get a positive we can sign it out and be done with it.” For specimens that are negative on DFA, the next step depends on the state of the patient’s immune system. For patients who are largely immunocompetent, shell vial culture is done. For immunocompromised patients—solid organ transplant recipients, oncology and ICU patients—Luminex can be ordered. “That seems to be working fairly well,” Dr. Valsamakis says.

“I wanted to restrict the number of patients getting Luminex to those who desperately needed it,” she explains. “When you change your paradigm back to the bad old days of conventional PCR, you run the risk of contamination, because many samples are chock full of virus. Most of us who had adopted real-time PCR went away from three-compartment setups to two compartments. Now we have to go back to more-complicated labs and train a whole new generation of technologists to handle amplicons.”

Dr. Valsamakis adopted Luminex because at the time it was the only option. However, she notes, “The pandemic generated a lot of support to allow a fast path through FDA for molecular H1N1 panels. Now we’re about to trial FilmArray.” Several instruments would be needed to overcome FilmArray’s low throughput, she acknowledges. Once you had them, “you could just keep pumping cartridges into these things. It could allow us to get rid of DFA completely in our high-risk population and offer FilmArray around the clock. It is so easy to use you could have MLT-level technologists load cartridges and have a certified MT at the end signing out. I think that’s kind of where the field is going.”

At Viracor-IBT, a molecular and immunodiagnostics laboratory, the Luminex platform has been used for respiratory viruses since 2008 because of the breadth of viruses the xTAG RVP detects, says vice president Steve Kleiboeker, PhD. Viracor-IBT used the platform to build a test that assists with differential diagnosis for immunocompromised populations.

But Dr. Kleiboeker doesn’t consider the xTAG RVP to be the in-house test for every need. “It’s a challenging method that is relatively complex,” he says. Moreover, “assay refinement may be required to account for ongoing seasonal and genetic variances.” A multiplex respiratory virus panel is not a standalone solution, he points out, because “many factors are at play for clinical practice.” For example, when there are known local outbreaks of influenza not requiring a full panel, Viracor-IBT uses its standalone, in-house–developed real-time PCR assay. In other cases, additional life-threatening respiratory infections may need to be evaluated, such as atypical bacterial pneumonias, cytomegalovirus, or invasive pulmonary aspergillosis.

At Evanston Hospital, Dr. Kaul and Dr. Thomson are evaluating eSensor and FilmArray, respectively. Their labs use now a variety of methods to detect single viruses: in-house real-time PCR assays for RSV and adenovirus; Eragen for flu A/B; DFA; and culture. “We’re looking for a technology that will allow us to do all these with a single step and a single method,” Dr. Thomson says. Dr. Kaul adds, “We would keep our in-house PCRs. In an outbreak it is very difficult and expensive to test everyone by multianalyte panels.”

They will compare in-house real-time PCR assays, FilmArray, and GenMark for workflow, cost, and performance and have a new approach for next season. “With GenMark we are seeing nice sensitivity,” Dr. Kaul says. “It is looking better than FilmArray for flu A/B. That’s our first take.”

Dr. Thomson says that selection of FilmArray, with its low throughput, “depends on how you position it.” One option is to use it for patients who are ill enough with respiratory disease to be admitted. “The volume of that work over 24 hours is not so great,” he says. “And a physician would have an answer by the time the patient gets to the ICU.” Combining the two platforms in a two-tier system might be possible, Dr. Kaul says. “We could use FilmArray for patients where an answer is needed urgently, knowing it will lack some sensitivity and we might have to repeat with real-time PCR.” GenMark would be for routine testing. Dr. Thomson says Nanosphere Verigene Respiratory Virus Plus could also function as part of a two-tier system. It is a two-step cartridge system that measures flu A/B and subtypes and RSV with very good sensitivity.

Because eSensor requires separate extraction and amplification steps, it should be used in a high-complexity lab with highly trained technologists, Dr. Kaul says. “The nice thing about FilmArray,” she says, “is that it is integrated and doesn’t require a highly trained technologist. We might trade some sensitivity for ease of use.” Though both GenMark and Luminex are open systems, Dr. Kaul finds GenMark to be much less work. “Luminex has so many manual steps there are many opportunities for contamination,” she adds.

Like Dr. Chapin, Dr. Thomson thinks about the interaction between multianalyte panels for respiratory viruses and bacterial superinfection. He is concerned that clinicians not lose their clinical acumen as laboratory tests become better. “We know that respiratory viruses predispose patients to secondary bacterial infections,” Dr. Thomson says. “We don’t want doctors to become too comfortable that the story is over if PCR is positive for a virus. It is possible that the patient has pneumococcal or staphylococcal infection on top of the virus. Unless you get additional testing, you could miss life-threatening disease.”

Like the others, Dr. Jerris of Children’s Healthcare of Atlanta is searching for the optimal test or combination of tests, saying, “We have a bit of everything right now.” Rather than offer a multianalyte panel, physicians in his system can choose which assays they want. “I’m trying to make the clinicians think a bit,” he says. He offers Cepheid for enterovirus testing and Prodesse for parainfluenza and human metapneumovirus. He recently implemented the Focus Simplexa flu A/B and RSV assays. Children’s has active solid organ and bone marrow transplant programs so quantitation is needed. FilmArray is under serious consideration now.

In a broader vein, Dr. Jerris says, “With the expanding variety of multiplex platforms, many of which are cleared, most laboratories can find something that meets their needs.” Where these assays will be performed is not yet entirely clear. “It may be the micro lab, the core lab, or point of care,” he says. “But we need flexibility in the laboratory of the future.”